mvpa2.misc.surfing.volsurf.VolSurfMinimalMapping¶

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class
mvpa2.misc.surfing.volsurf.
VolSurfMinimalMapping
(vg, white, pial, intermediate=None, nsteps=10, start_fr=0.0, stop_fr=1.0, start_mm=0, stop_mm=0)¶ Represents the minimal mapping from nodes to voxels. ‘minimal’, in this context, means that the mapping from voxels to nodes is many-to-one (i.e. each voxel is associated with at most one node)
Each voxel can be associated with just a single node.
Parameters: volgeom: volgeom.VolGeom
Volume geometry
white: surf.Surface
Surface representing white-grey matter boundary
pial: surf.Surface
Surface representing pial-grey matter boundary
intermediate: surf.Surface (default: None).
Surface representing intermediate surface. If omitted it is the node-wise average of white and pial.
nsteps: int (default: 10)
Number of steps from white to pial surface
start_fr: float (default: 0)
Relative start position of line in gray matter, 0.=white surface, 1.=pial surface.
stop_fr: float (default: 1)
Relative stop position of line (as in see start).
start_mm: float (default: 0)
Absolute start position offset (as in start_fr).
stop_mm: float (default: 0)
Absolute start position offset (as in start_fr).
Notes
‘pial’ and ‘white’ should have the same topology.
Attributes
intermediate_surface
Returns the node-wise average of the pial and white surface pial_surface
Returns the pial surface volgeom
Returns the volume geometry white_surface
Returns the white surface Methods
coordinates_to_grey_distance_mm
(nodes, xyz)Computes the grey position of coordinates in metric units get_node2voxels_mapping
()Returns: get_parameter_dict
()Returns a dictionary with the most important parameters of this instance surf_project_nodewise
(xyz)Projects coordinates on lines connecting pial and white matter. surf_project_weights
(nodes, xyz)Computes relative position of xyz on lines from pial to white matter. surf_project_weights_nodewise
(xyz)Computes relative position of xyz on lines from pial to white matter. surf_unproject_weights_nodewise
(weights)Maps relative positions in grey matter to coordinates voxel_count_nifti_image
()Returns a NIFTI image indicating how often each voxel is selected. -
get_node2voxels_mapping
()¶ Returns: n2v: dict
A mapping from node indices to voxels. In this mapping, the
‘i’-th node is associated with ‘n2v[i]=v2p’ which contains the
mapping from linear voxel indices to grey matter positions. In
other words, ‘n2v[i][idx]=v2p[idx]=pos’ means that the voxel with
linear index ‘idx’ is associated with node ‘i’ and has has
relative position ‘pos’ in the gray matter.
If node ‘i’ is outside the volume, then ‘n2v[i]=None’.
Notes
The typical use case is selecting voxels in the grey matter. The rationale of this method is that (assuming a sufficient dense cortical surface mesh, combined with a sufficient number of nsteps, the grey matter is sampled dense enough so that ‘no voxels are left out’.
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